Research, development, and application of technologiesIntelligent data analysis and modelling


MultipluginG is an effective plugin extension of software Geneious addressing manipulation with data obtained from NextGen sequencing. The software is implemented especially for data obtained from DNA sequencers prone to base insertion and deletion errors during base calling , however the functionality can be a great help even for other types of DNA sequencers.

Software MultipluginG enables:

  • Identification of reads, which cover approximately the same area of the reference sequence (further referred as amplicon groups). The software is able to quickly sort individual reads even if their parts overlap.
  • Filtering multiple alignment based on percentual gap ratio in positions with a gap in the reference sequence. Filter is applied sequentially on each amplicon group in the column. This functionality automates deletion of columns with a small number of bases and a gap in the reference sequence, which are a consequence of insertion errors during base calling.
  • Identification and replacement of multiple alignment columns based on percentual gap ratio of bases differing from the reference base. Filter is applied sequentially on each amplicon group in the column. If the number of different bases does not reach a specified threshold, all bases in the column of the amplicon group are replaced with the reference base. This functionality simplifies the resulting alignment and corrects base calling errors.
  • Displaying the positions of filtered columns and numbers of replaced bases in a graph over the reference sequence.
  • Displaying statistics for individual columns of an alignment (by moving the mouse cursor over the column) in a separate tooltip window. A separate statistics are displayed for each amplicon group.
  • Displaying column statistics for amplicon groups sorted by the number of mutations in a separate table. The table can be filtered to view only CDS positions.
  • Sorting and filtering alignments according to the direction of reads.

For more information please click here.

For information about pricing and to obtain a free trial version please contact us at

MultipluginG – screenshots


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